BEAST v2.7.8 Documentation: beastlabs.evolution.tree.ConstrainedClusterTree

BEASTObject that performs calculations based on the State.
A node that can be part of the state.
Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data.
Create initial beast.tree by hierarchical clustering, either through one of the classic link methods or by neighbor joining. The following link methods are supported:
o single link,
o complete link,
o UPGMA=average link,
o mean link,
o centroid,
o Ward and
o adjusted complete link
o neighborjoining
o neighborjoining2 - corrects tree for tip data, unlike plain neighborjoining

Logable: yes, this can be used in a log.

Inputs:

constraint, constraints, minBranchLength, clusterType, taxa, distance, clock.rate, initial, trait, taxonset, nodetype, adjustTreeNodeHeights, estimate